Add the flours, espresso powder, baking soda, baking powder, and salt to a bowl. Whisk for about 20 seconds until fully mixed. Add all the chocolate and mix until chocolate is coated in flour. Set the bowl aside.
In a large bowl or stand mixer with the paddle attachment, beat the brown butter and butter for 1 minute until combined. Scrape the sides. Add the white and brown sugars. Beat for 5 minutes on medium-high speed, until fluffy and lighter in color. Scrape the bowl once halfway (at around 2 minutes) and once at the end (after about 5 minutes).
Add the egg, egg yolk, vanilla extract, and butter and nut flavoring. Beat on the second-highest speed for 6-10 minutes. Scrape the bowl and paddle every few minutes, making sure every bit gets incorporated.
Add the flour and chocolate mixture to the bowl. Mix on the lowest speed or hand-mix with a silicone spatula until there’s no more dry flour present.
Immediately scoop the dough into 80-gram or ¼-cup balls***. Shape the dough into pucks and place each puck on a baking sheet or plate. Repeat until all the dough is gone (12-13 pucks). Wrap the baking sheet tightly and cool in the refrigerator for 12 hours. (In a pinch, 30 minutes in the freezer is fine!)
When ready to bake, preheat the oven to 350°F***, and remove the dough pucks from the refrigerator. Allow the oven to preheat for about 30 minutes, while the dough rests on the counter.
Place the cookies on a parchment- or silicone-lined cookie sheet, 2 inches apart. Bake for 13-15 minutes on the middle rack, just until the edges are barely browned and the center of the cookie no longer looks glossy.
Remove cookies from the oven. Allow to cool or enjoy hot with milk or ice cream.